No, neither you guys said work. It still report the same error. 在 2014年3月27日星期四UTC+8下午11时11分07秒，David Shteynberg写道： > > Actually it failed because it wasn't run in Semiparametric mode. Check > the box next to use nonparametric models and try again. > On Mar 27, 2014 7:27 AM, "Jimmy Eng" <[email protected] <javascript:>> > wrote: > >> I believe that PeptideProphet failed because you told it to use a decoy >> tag that it could not find in any of the search results. Apparently the >> decoy tag in MSGF+ is always "XXX_" and can't be changed. So you must set >> that as the decoy tag and make sure that same decoy tag is used in >> MyriMatch. >> >> Another option is to use a self generated target-decoy database and turn >> off the auto-decoy option in the search engines. >> >> >> On Thu, Mar 27, 2014 at 2:29 AM, <[email protected] <javascript:>>wrote: >> >>> Hi, >>> I try to combine two different search engine results using iProphet. >>> One is myrimatch, the other is MSGF+. >>> The decoy database search is auto conducted by each search engine. >>> But iProphet failed, exactly PeptideProphetParser failed, when I >>> select "Analysis Pipeline (Tandem)" -> "Analyze Peptides" in TPP 4.6.3 >>> to combine them. >>> The parameters for PeptideProphet and InterProphet are showed below. >>> >>> >>> <https://lh6.googleusercontent.com/-aIAyfalUSIo/UzPtqmRkHoI/AAAAAAAAAAM/RcNaJf-gpcU/s1600/QQ%E5%9B%BE%E7%89%8720140327172121.jpg> >>> >>> >>> <https://lh5.googleusercontent.com/-rfMJq_uvl4c/UzPt7QykkQI/AAAAAAAAAAU/DGzmgdsYqhQ/s1600/QQ%E5%9B%BE%E7%89%8720140327172230.jpg> >>> >>> Here is the log. >>> >>> running: "C:/Inetpub/tpp-bin/PeptideProphetParser >>> "interact.pep.xml" MINPROB=0.01 DECOY=###REV###" >>> >>> Using Decoy Label "###REV###". >>> (MS-GF+) >>> WARNING!! The discriminant function for MSGFPL is not yet complete. It is >>> presented here to help facilitate trial and discussion. Reliance on this >>> code for publishable scientific results is not recommended. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>> which relies on a DECOY search. >>> init with MS-GF+ trypsin >>> two different search engines specified: MS-GF+ and MyriMatch >>> >>> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >>> MINPROB=0.01 DECOY=###REV###" failed: Operation not permitted >>> >>> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >>> MINPROB=0.01 DECOY=###REV###" exited with non-zero exit code: 1 >>> QUIT - the job is incomplete >>> >>> >>> Can any body tell me why this happen? Why the PeptideProphetParser >>> failed? >>> >>> By the way, it didn't print error information when I try the command >>> manually. >>> Thanks very much! >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected] <javascript:>. >>> To post to this group, send email to >>> [email protected]<javascript:> >>> . >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> >
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